From 31fc64f82cc5fc87cc4764f4ce05c0f53ea00a76 Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Mon, 14 Mar 2016 13:17:29 -0400
Subject: [PATCH] To address weird case with all hom-refs, but alt allele is
 present, skip AS_QD for all-ref sites and remove raw annotations whether or
 not they can be successfully finalized

---
 .../gatk/tools/walkers/annotator/AS_QualByDepth.java          | 2 ++
 .../gatk/tools/walkers/annotator/VariantAnnotatorEngine.java  | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java
index e4c806e6a..8df281d72 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java
@@ -172,6 +172,8 @@ public class AS_QualByDepth extends InfoFieldAnnotation implements ReducibleAnno
             return null;
 
         final List<Integer> standardDepth = getAlleleDepths(genotypes);
+        if (standardDepth == null) //all no-calls and homRefs
+            return null;
 
         //Parse the VC's allele-specific qual values
         List<Object> alleleQualObjList = vc.getAttributeAsList(GATKVCFConstants.AS_QUAL_KEY);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
index d62029fb3..e8394cec4 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
@@ -357,9 +357,9 @@ public class VariantAnnotatorEngine {
             final Map<String, Object> annotationsFromCurrentType = currentASannotation.finalizeRawData(vc, originalVC);
             if ( annotationsFromCurrentType != null ) {
                 infoAnnotations.putAll(annotationsFromCurrentType);
-                //clean up raw annotation data after annotations are finalized
-                infoAnnotations.remove(currentASannotation.getRawKeyName());
             }
+            //clean up raw annotation data after annotations are finalized
+            infoAnnotations.remove(currentASannotation.getRawKeyName());
         }
 
         // generate a new annotated VC